Identification of acquired antimicrobial resistance genes
Ea Zankari,Henrik Hasman,Salvatore Cosentino,Martin Vestergaard,Simon Rasmussen,Ole Lund,Frank Møller Aarestrup,Mette Voldby Larsen +7 more
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TLDR
A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created, and the method was evaluated on WGS chromosomes and plasmids of 30 isolates.Abstract:
Objectives
Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. Thus, the current challenge is to extract the relevant information from the large amount of generated data.read more
Citations
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Journal ArticleDOI
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
Sushim K. Gupta,Babu Roshan Padmanabhan,Seydina M. Diene,Rafael López-Rojas,Marie Kempf,Luce Landraud,Jean-Marc Rolain +6 more
TL;DR: A concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR geneticeterminants is created.
Journal ArticleDOI
Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli
Katrine Grimstrup Joensen,Flemming Scheutz,Ole Lund,Henrik Hasman,Rolf Sommer Kaas,Eva Møller Nielsen,Frank Møller Aarestrup +6 more
TL;DR: A real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli found whole-genome sequencing typing is a superior alternative to conventional typing strategies and may also be applied to typing and Surveillance of other pathogens.
Journal ArticleDOI
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
H. Bjørn Nielsen,Mathieu Almeida,Agnieszka S. Juncker,Simon Rasmussen,Junhua Li,Shinichi Sunagawa,Damian R. Plichta,Laurent Gautier,Anders Gorm Pedersen,Eric Pelletier,Ida Bonde,Trine Nielsen,Chaysavanh Manichanh,Manimozhiyan Arumugam,Jean-Michel Batto,Marcelo B Quintanilha dos Santos,Nikolaj Blom,Natalia Borruel,Kristoffer Sølvsten Burgdorf,Fouad Boumezbeur,Francesc Casellas,Joël Doré,Piotr Dworzynski,Francisco Guarner,Torben Hansen,Falk Hildebrand,Rolf Sommer Kaas,Sean Kennedy,Karsten Kristiansen,Jens Roat Kultima,Pierre Leonard,Florence Levenez,Ole Lund,Bouziane Moumen,Denis Le Paslier,Nicolas Pons,Oluf Pedersen,Edi Prifti,Junjie Qin,Jeroen Raes,Søren J. Sørensen,Julien Tap,Sebastian Tims,David W. Ussery,Takuji Yamada,Pierre Renault,Thomas Sicheritz-Pontén,Peer Bork,Jun Wang,Søren Brunak,S. Dusko Ehrlich +50 more
TL;DR: This work presents a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences.
Journal ArticleDOI
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Michael Inouye,Harriet Dashnow,Harriet Dashnow,Lesley Raven,Mark B. Schultz,Bernard J. Pope,Bernard J. Pope,Takehiro Tomita,Justin Zobel,Kathryn E. Holt +9 more
TL;DR: This work presents SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data, which is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment.
Journal ArticleDOI
What is a resistance gene? Ranking risk in resistomes.
TL;DR: Rules are proposed for estimating the risks associated with genes that are present in environmental resistomes by evaluating the likelihood of their introduction into human pathogens, and the consequences of such events for the treatment of infections.
References
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Journal ArticleDOI
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Mette Voldby Larsen,Salvatore Cosentino,Simon Rasmussen,Carsten Friis,Henrik Hasman,Rasmus L. Marvig,Lars Jelsbak,Thomas Sicheritz-Pontén,David W. Ussery,Frank Møller Aarestrup,Ole Lund +10 more
TL;DR: A Web-based method for MLST of 66 bacterial species based on whole-genome sequencing data that enables investigators to determine the sequence types of their isolates on the basis of WGS data.
Journal ArticleDOI
Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes.
TL;DR: A preliminary assessment of the amino acids which may be important in binding aminoglycosides was obtained from data and from the results of mutational analysis of several of the genes encoding am inoglycoside-modifying enzymes.
Journal ArticleDOI
Acquired Antibiotic Resistance Genes: An Overview
Angela H.A.M. van Hoek,Dik Mevius,Dik Mevius,Beatriz Guerra,Peter Mullany,Adam P. Roberts,Henk Aarts +6 more
TL;DR: Attention is paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.
Journal ArticleDOI
Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
Lance B. Price,Marc Stegger,Henrik Hasman,Maliha Aziz,Jesper Larsen,Paal Skytt Andersen,Talima Pearson,Andrew E. Waters,Jeffrey T. Foster,James M. Schupp,John D. Gillece,Elizabeth M. Driebe,Cindy M. Liu,Cindy M. Liu,Burkhard Springer,Irena Zdovc,Antonio Battisti,Alessia Franco,Jacek Żmudzki,Stefan Schwarz,Patrick Butaye,Eric Jouy,Constança Pomba,M. Concepción Porrero,Raymond Ruimy,Tara C. Smith,D. Ashley Robinson,J. Scott Weese,Carmen Sofia Arriola,Fangyou Yu,Frédéric Laurent,Paul Keim,Paul Keim,Robert Skov,Frank Møller Aarestrup +34 more
TL;DR: The results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA, which appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance.
Journal ArticleDOI
Comparison of antimicrobial resistance phenotypes and resistance genes in Enterococcus faecalis and Enterococcus faecium from humans in the community, broilers, and pigs in Denmark.
TL;DR: Differences in the occurrence of resistance and tetracycline resistance genes were observed among isolates from the different sources, however, similar resistance patterns and resistant genes were detected frequently indicating that transmission of resistant enterococci or resistance genes takes place between humans, broilers, and pigs.
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